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Responses, Enhances Secondary Immune Responses, and Abrogates Autoimmunity During Tumor Immunotherapy","volume":"21","author":"BW Bridle","year":"2013","journal-title":"Molecular Therapy"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"9578","DOI":"10.1073\/pnas.0400567101","article-title":"Induction of interferon-stimulated gene expression and antiviral responses require protein deacetylase activity","volume":"101","author":"H-M Chang","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.tcb.2010.10.003","article-title":"EHD proteins: key conductors of endocytic transport","volume":"21","author":"N Naslavsky","year":"2011","journal-title":"Trends Cell Biol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"19122","DOI":"10.1074\/jbc.M808233200","article-title":"The tyrosine kinase c-Src enhances RIG-I (retinoic acid-inducible gene I)-elicited antiviral 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K\u00f6nig","year":"2010","journal-title":"Nature"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"1243","DOI":"10.1016\/j.cell.2009.12.017","article-title":"The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus","volume":"139","author":"AL Brass","year":"2009","journal-title":"Cell"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"1410","DOI":"10.4049\/jimmunol.0901709","article-title":"Critical role of IL-1 receptor-associated kinase-M in regulating chemokine-dependent deleterious inflammation in murine influenza pneumonia","volume":"184","author":"M Seki","year":"2010","journal-title":"J Immunol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1089\/ars.2011.4253","article-title":"BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion","volume":"18","author":"P Willems","year":"2013","journal-title":"Antioxid Redox 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Research"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1016\/j.immuni.2006.03.022","article-title":"HS1 functions as an essential actin-regulatory adaptor protein at the immune synapse","volume":"24","author":"TS Gomez","year":"2006","journal-title":"Immunity"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"3631","DOI":"10.1073\/pnas.90.8.3631","article-title":"Identification of HS1 protein as a major substrate of protein-tyrosine kinase(s) upon B-cell antigen receptor-mediated signaling","volume":"90","author":"Y Yamanashi","year":"1993","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"6572","DOI":"10.4049\/jimmunol.0904203","article-title":"Hoxa9 regulates Flt3 in lymphohematopoietic progenitors","volume":"185","author":"K Gwin","year":"2010","journal-title":"J Immunol"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"15209","DOI":"10.1073\/pnas.011503998","article-title":"Aberrant 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Rev"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nrc2780","article-title":"Fibroblast growth factor signalling: from development to cancer","volume":"10","author":"N Turner","year":"2010","journal-title":"Nat Rev Cancer"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"e0124651","DOI":"10.1371\/journal.pone.0124651","article-title":"A Functional Role of Fibroblast Growth Factor Receptor 1 (FGFR1) in the Suppression of Influenza A Virus Replication","volume":"10","author":"X Liu","year":"2015","journal-title":"PLoS One"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1038\/nri3109","article-title":"Strategies to discover regulatory circuits of the mammalian immune system","volume":"11","author":"I Amit","year":"2011","journal-title":"Nat Rev Immunol"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"1869","DOI":"10.1101\/gr.173039.114","article-title":"Linking signaling pathways to transcriptional programs in breast cancer","volume":"24","author":"HU Osmanbeyoglu","year":"2014","journal-title":"Genome Res"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1021\/pr501138h","article-title":"Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics","volume":"14","author":"B-JM Webb-Robertson","year":"2015","journal-title":"J Proteome Res"},{"key":"ref83","first-page":"026831","article-title":"Widespread shortening of 3' untranslated regions and increased exon inclusion characterize the human macrophage response to infection","author":"AA Pai","year":"2015","journal-title":"bioRxiv"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"e01174","DOI":"10.1128\/mBio.01174-14","article-title":"Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses","volume":"5","author":"VD Menachery","year":"2014","journal-title":"MBio"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1186\/1752-0509-5-190","article-title":"Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems","volume":"5","author":"JE McDermott","year":"2011","journal-title":"BMC Systems Biology"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/ng.3259","article-title":"Understanding multicellular function and disease with human tissue-specific networks","volume":"47","author":"CS Greene","year":"2015","journal-title":"Nat Genet"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"e1004220","DOI":"10.1371\/journal.pcbi.1004220","article-title":"Sharing and Specificity of Co-expression Networks across 35 Human Tissues","volume":"11","author":"E Pierson","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1016\/j.cell.2010.01.044","article-title":"An atlas of combinatorial transcriptional regulation in mouse and man","volume":"140","author":"T Ravasi","year":"2010","journal-title":"Cell"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"5748","DOI":"10.1021\/pr1005247","article-title":"Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data","volume":"9","author":"B-JM Webb-Robertson","year":"2010","journal-title":"J Proteome Res"},{"key":"ref90","first-page":"69","article-title":"A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components","volume":"13","author":"SA Knaack","year":"2014","journal-title":"Cancer Informatics"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nature Genetics"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"A Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"A Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nature03441","article-title":"Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals","volume":"434","author":"X Xie","year":"2005","journal-title":"Nature"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkt997","article-title":"JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles","volume":"42","author":"A Mathelier","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: scanning for occurrences of a given motif","volume":"27","author":"CE Grant","year":"2011","journal-title":"Bioinformatics"},{"key":"ref97","article-title":"Reactome: a database of reactions, pathways and biological processes","volume":"39","author":"D Croft","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"D199","DOI":"10.1093\/nar\/gkt1076","article-title":"Data, information, knowledge and principle: back to metabolism in KEGG","volume":"42","author":"M Kanehisa","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1016\/j.meegid.2009.07.006","article-title":"Systems-based candidate genes for human response to influenza infection","volume":"9","author":"L Zhang","year":"2009","journal-title":"Infect Genet Evol"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1038\/nature07151","article-title":"Drosophila RNAi screen identifies host genes important for influenza virus replication","volume":"454","author":"L Hao","year":"2008","journal-title":"Nature"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/j.virol.2009.02.046","article-title":"The use of Random Homozygous Gene Perturbation to identify novel host-oriented targets for influenza","volume":"387","author":"B Sui","year":"2009","journal-title":"Virology"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"e1003440","DOI":"10.1371\/journal.ppat.1003440","article-title":"The Interactomes of Influenza Virus NS1 and NS2 Proteins Identify New Host Factors and Provide Insights for ADAR1 Playing a Supportive Role in Virus Replication","volume":"9","author":"B de Chassey","year":"2013","journal-title":"PLOS Pathogens"},{"key":"ref103","doi-asserted-by":"crossref","first-page":"13010","DOI":"10.1128\/JVI.02651-10","article-title":"Generation and comprehensive analysis of an influenza virus polymerase cellular interaction network","volume":"85","author":"L Tafforeau","year":"2011","journal-title":"J Virol"},{"key":"ref104","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1016\/j.bbagrm.2008.04.006","article-title":"Identification of interleukin-1 and interleukin-6-responsive genes in human monocyte-derived macrophages using microarrays","volume":"1779","author":"J Jura","year":"2008","journal-title":"Biochimica et Biophysica Acta (BBA)\u2014Gene Regulatory Mechanisms"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"D1228","DOI":"10.1093\/nar\/gks1147","article-title":"InnateDB: systems biology of innate immunity and beyond\u2014recent updates and continuing curation","volume":"41","author":"K Breuer","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref106","doi-asserted-by":"crossref","first-page":"D726","DOI":"10.1093\/nar\/gku967","article-title":"The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease","volume":"43","author":"JT Eppig","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref107","author":"DJ Sheskin","year":"2003"},{"key":"ref108","doi-asserted-by":"crossref","first-page":"D808","DOI":"10.1093\/nar\/gks1094","article-title":"STRING v9.1: protein-protein interaction networks, with increased coverage and integration","volume":"41","author":"A Franceschini","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref109","doi-asserted-by":"crossref","first-page":"e31826","DOI":"10.1371\/journal.pone.0031826","article-title":"HIPPIE: Integrating protein interaction networks with experiment based quality scores. 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